Whiteshark, you said you are or were using a Logitech Extreme 3d Pro? I think I have the same issue, or something similar. I will look further tonight. From my memory I think that the 3d Pro is a one-way stick. I'll get back to you later.

EDIT: in release 2, issuing the ToggleOneWayYaw stops the automatic X axis movement in game, however, I can't map anything in the controller options. As soon as I click on something, RightX populates the field.
EDIT 2: yeah, I can't get the Roll (Z axis) to work. It doesn't get recognized. I got everything else mapped. Also, if I am not holding my stick in the direction I want to map, RightX populates the field as soon as I click on the axis to bind and the commands don't seem to make a difference.
EDIT 3: I was able to get the twist working with Joy2Key (Thanks Sarge). Mapped it to the q and e keys. Not analog, but at least works for now. Let us know if you need more information to troubleshoot this.